Table 3

Top DMCs and the corresponding differential gene expression in CD19+ B cells in patients with primary Sjögren's syndrome (pSS) and healthy controls

CpG siteGene symbolGene nameInterferon-inducedCpG island informationGene propertyEnhancer*Promoter†Methylation Δβ‡Methylation
p value§
Expression log2 (FC)¶Expression
p value**
cg21549285MX1MX dynamin-like GTPase 1YesShore5′UTRNoYes−0.342.3×10−111.97<5×10−5
cg05696877IFI44LInterferon-induced protein 44-likeYesOpen sea5′UTRNoNo−0.333.8×10−203.79<5×10−5
cg03607951IFI44LInterferon-induced protein 44-likeYesOpen seaTSS1500YesYes−0.302.6×10−183.79<5×10−5
cg23570810IFITM1Interferon-induced transmembrane protein 1YesShoreGene bodyYesNo−0.261.3×10−101.63<5×10−5
cg05552874IFIT1Interferon-induced protein with tetratricopeptide repeats 1YesOpen seaGene bodyYesYes−0.262.1×10−164.44<5×10−5
cg06981309PLSCR1Phospholipid scramblase 1YesShore5′UTRNoYes−0.252.3×10−121.64<5×10−5
cg14293575USP18Ubiquitin-specific peptidase 18YesShelf5′UTRNoNo−0.259.7×10−143.27<5×10−5
cg03038262IFITM1Interferon-induced transmembrane protein 1YesShore3′UTRYesNo−0.252.9×10−101.63<5×10−5
cg22930808PARP9Poly (ADP-ribose) polymerase family, member 9YesShore5′UTRYesNo−0.242.4×10−101.89<5×10−5
cg00959259PARP9Poly (ADP-ribose) polymerase family, member 9YesShore5′UTRYesNo−0.241.3×10−131.89<5×10−5
cg22862003MX1MX dynamin-like GTPase 1YesShoreTSS1500YesYes−0.225.8×10−121.97<5×10−5
cg10549986RSAD2Radical S-adenosyl methionine domain containing 2YesOpen seaFirst exonYesYes−0.211.4×10−173.19<5×10−5
cg16810031ZPBP2Zona pellucida binding protein 2NoCpG islandTSS1500YesNo0.217.4×10−8n.a.n.a.
cg25330422STAT3Signal transducer and activator of transcription 3YesShelf3′UTRYesYes0.223.2×10−13-0.09n.s.
  • *Genomic location of differentially methylated CpG site (DMC) overlapping H3K4me1 (poised enhancer mark) and/or H3K27ac (active enhancer mark) peak in reference CD19+ B cells.

  • †Genomic location of DMC overlapping H3K4me3 (active promoter mark) peak in reference CD19+ B cells.

  • ‡Methylation Δβ refers to the difference in mean methylation β (β-values) between patients with pSS and healthy controls. A negative Δβ represents hypomethylation in the patients.

  • §p Value of the association between CpG methylation and pSS (significance threshold p<1.3×10−7; Bonferroni corrected).

  • ¶Differential gene expression as log2(FC) between patients with pSS and healthy controls.

  • **p Value of differential gene expression between patients with pSS and healthy controls.

  • FC, fold change; n.a., not available; n.s., not significant; TSS, transcription start site.